The problem

If you're using a PWM controlled fan with a low minimal speed together with
a Supermicro motherboard there's a good chance that the fan speed will be go
up and down the whole time, while the system generates lots of critical fan
alerts.

The reason for this is that these boards are build for servers in a datacenter,
and these machines would overheat fast if their often small but very fast
turning fans would stop working.

The solution

You can use IPMI software to change the lower fan speed limit to a lower value.